[phenixbb] MR-SAD, SAD

Terwilliger, Thomas Charles terwilliger at lanl.gov
Mon Jan 26 07:19:15 PST 2015

Hi Francis,

An estimated RMSD is used in the calculation in Phaser.  You can specify 

   partpdb_rms = 1

to define the estimated RMSD between model and true structure that is used when Phaser is called by autosol.  The default is 1 A.  I think there is no way at present to tell Phaser about incompleteness, at least autosol does not have a keyword for it (Randy may be able to comment on that...)

All the best,
Tom T

From: Francis Reyes [reyesf at colorado.edu] on behalf of Francis Reyes [Francis.Reyes at Colorado.EDU]
Sent: Monday, January 26, 2015 8:13 AM
To: Terwilliger, Thomas Charles
Cc: phenixbb at phenix-online.org
Subject: Re: [phenixbb] MR-SAD, SAD

Hi Tom,

How is the input MR model treated when computing the HL's for the substructure search?

That is to say, how are errors in the MR solution taken into account or is the input model treated as being correct?

Errors being: positional errors, or model incompleteness errors?



On Jan 25, 2015, at 3:06 PM, Terwilliger, Thomas Charles <terwilliger at lanl.gov> wrote:

> If everything were ideal, then an MR solution, even if very distant and contributing very little phase information, should improve the Phaser identification of the sub-structure.  Therefore as you imagine, including it should have improved the situation.  In real life there is a lot of noise in the system, so small changes can sometimes make the difference between finding sites and not. Also the default parameters for Phaser sub-structure identification are not exactly the same for MR-SAD and for extreme defaults in autosol.

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